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Team:KULeuven/Model/Filter
From 2008.igem.org
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation rates | ! colspan="4" style="border-bottom: 1px solid #003E81;" | Degradation rates | ||
|- | |- | ||
| - | | d<sub> | + | | d<sub>pT7 tag</sub> |
| 0.00155 s<sup>-1</sup> | | 0.00155 s<sup>-1</sup> | ||
| UmuD tag added to speed up degradation of otherwise too stable T7 polymerase | | UmuD tag added to speed up degradation of otherwise too stable T7 polymerase | ||
| [http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation link] | | [http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation link] | ||
|- | |- | ||
| - | | d<sub> | + | | d<sub>mRNA RIBOKEY</sub> |
| 0.00462 s<sup>-1</sup> | | 0.00462 s<sup>-1</sup> | ||
| | | | ||
|[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | ||
|- | |- | ||
| - | | d<sub> | + | | d<sub>closed mRNA T7</sub> |
| 0.00462 s<sup>-1</sup> | | 0.00462 s<sup>-1</sup> | ||
| | | | ||
|[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | ||
|- | |- | ||
| - | | d<sub> | + | | d<sub>open mRNA T7</sub> |
| 0.00231 s<sup>-1</sup> | | 0.00231 s<sup>-1</sup> | ||
| | | | ||
|[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | ||
|- | |- | ||
| - | | d<sub> | + | | d<sub>open mRNA T7 complex</sub> |
| 0.00231 s<sup>-1</sup> | | 0.00231 s<sup>-1</sup> | ||
| | | | ||
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! colspan="4" style="border-bottom: 1px solid #003E81;" | Equilibrium constants | ! colspan="4" style="border-bottom: 1px solid #003E81;" | Equilibrium constants | ||
|- | |- | ||
| - | | K<sub> | + | | K<sub>eq 1</sub> |
| 0,015 [M] | | 0,015 [M] | ||
| between closed and open T7 mRNA, experimental | | between closed and open T7 mRNA, experimental | ||
| [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link] | | [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link] | ||
|- | |- | ||
| - | | K<sub> | + | | K<sub>eq 2</sub> |
| 0.0212 [M] | | 0.0212 [M] | ||
| between closed T7 mRNA and key unlocked mRNA complex, experimental | | between closed T7 mRNA and key unlocked mRNA complex, experimental | ||
| Line 93: | Line 93: | ||
| | | | ||
|- | |- | ||
| - | | k<sub> | + | | k<sub>mRNA T7</sub> |
| 0,0011 s<sup>-1</sup> | | 0,0011 s<sup>-1</sup> | ||
| | | | ||
Revision as of 14:14, 27 August 2008
dock/undock dropdown
Contents |
Filter
Position in the system
The filter is positioned immediately after the input, because its job is to filter out possible noise signals or background signals that aren't caused by the "desease". It is the starting piece of the whole system, situated before the invertimer- and the reset-subsystem.
Describing the system
see also: Project:Filter
ODE's
Parameters
| Name | Value | Comments | Reference |
|---|---|---|---|
| Degradation rates | |||
| dpT7 tag | 0.00155 s-1 | UmuD tag added to speed up degradation of otherwise too stable T7 polymerase | [http://www.openwetware.org/wiki/IGEM:Tsinghua/2007/Projects/RAP#Model_and_simulation link] |
| dmRNA RIBOKEY | 0.00462 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dclosed mRNA T7 | 0.00462 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dopen mRNA T7 | 0.00231 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| dopen mRNA T7 complex | 0.00231 s-1 | [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=124983&blobtype=pdf link] | |
| Equilibrium constants | |||
| Keq 1 | 0,015 [M] | between closed and open T7 mRNA, experimental | [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link] |
| Keq 2 | 0.0212 [M] | between closed T7 mRNA and key unlocked mRNA complex, experimental | [http://parts2.mit.edu/wiki/index.php/Berkeley2006-RiboregulatorsMain link] |
| Rate constants | |||
| kdis | 100 s-1 | derived from experimental values | |
| kcomplex | 57 s-1 | derived from experimental values | |
| Transcription rates | |||
| TetR_var_transcr_rate | p(TetR) dependent | (RiboKey) between 5E-5 and 0.0125 s-1 ~ [aTc] | |
| kmRNA T7 | 0,0011 s-1 | ||
Remark: The key-lock system has been enhanced to 0.3%-14% (todo: new parameters will be added in a new overview)
Models
CellDesigner (SBML file)
Matlab (SBML file)
Simulations
1. AND gate of the filter
In the simulation we can clearly see this series of events:
- when dark blue(ribokey) starts to increase, red (T7) also starts to increase, giving rise to an increasing amount of lactonase (blue) = AND-GATE.
- when dark blue(ribokey) starts to decrease, red (T7) also starts to decrease, but much slower. The lactonase also starts to decrease, as it should be.
The short lifetime of the ribokey compared to the lifetime of the T7-protein, guarantees that the AND-GATE always works perfectly fine: when there's no more input, the ribokey will rapidly decrease (and disappear) and makes sure that the AND-GATE is not activated anymore, even when the T7-protein is slowly decreasing.
2. Filtering in practice
In the simulation three kinds of inputpulses have been used:
- First pulse: 300s
- small peak of lactonase
- no influence on the timer
- Second pulse: 1000s
- medium peak of lactonase
- influences the timer by levelling the timing capabilities, but it doesn't reset the timer
- Third pulse: 5000s
- huge peak of lactonase
- reset of the timer: amount of complex goes to zero
Sensitivity Analysis
